% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/EdgeRAnalyze.R
\name{edgeR_analyze}
\alias{edgeR_analyze}
\title{Differential Gene Expression Analysis using 'edgeR'}
\usage{
edgeR_analyze(
  tumor_file,
  normal_file,
  output_file,
  logFC_threshold = 2.5,
  p_value_threshold = 0.01
)
}
\arguments{
\item{tumor_file}{Path to the tumor data file (RDS format).}

\item{normal_file}{Path to the normal data file (RDS format).}

\item{output_file}{Path to save the output DEG data (RDS format).}

\item{logFC_threshold}{Threshold for log fold change for marking up/down-regulated genes.}

\item{p_value_threshold}{Threshold for p-value for filtering significant genes.}
}
\value{
A data frame of differential expression results.
}
\description{
This function performs differential gene expression analysis using the 'edgeR' package.
It reads tumor and normal expression data, merges them, filters low-expressed genes,
normalizes the data, performs edgeR analysis, and outputs the results along with information
on gene expression changes.
}
\examples{
# Define file paths for tumor and normal data from the data folder
tumor_file <- system.file("extdata",
                         "removebatch_SKCM_Skin_TCGA_exp_tumor_test.rds",
                         package = "TransProR")
normal_file <- system.file("extdata",
                           "removebatch_SKCM_Skin_Normal_TCGA_GTEX_count_test.rds",
                           package = "TransProR")
output_file <- file.path(tempdir(), "DEG_edgeR.rds")

DEG_edgeR <- edgeR_analyze(
  tumor_file = tumor_file,
  normal_file = normal_file,
  output_file = output_file,
  2.5,
  0.01
)

# View the top 5 rows of the result
head(DEG_edgeR, 5)

}
\references{
edgeR: Differential analysis of sequence read count data.
For more information, visit the edgeR Bioconductor page:
https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
}